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Microsatellite analysis in the genome of Acanthaceae: An in silico approach

BACKGROUND: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to...

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Autores principales: Kaliswamy, Priyadharsini, Vellingiri, Srividhya, Nathan, Bharathi, Selvaraj, Saravanakumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Medknow Publications & Media Pvt Ltd 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329617/
https://www.ncbi.nlm.nih.gov/pubmed/25709226
http://dx.doi.org/10.4103/0973-1296.149731
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author Kaliswamy, Priyadharsini
Vellingiri, Srividhya
Nathan, Bharathi
Selvaraj, Saravanakumar
author_facet Kaliswamy, Priyadharsini
Vellingiri, Srividhya
Nathan, Bharathi
Selvaraj, Saravanakumar
author_sort Kaliswamy, Priyadharsini
collection PubMed
description BACKGROUND: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. OBJECTIVE: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. MATERIALS AND METHODS: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. RESULTS: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. CONCLUSION: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.
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spelling pubmed-43296172015-02-23 Microsatellite analysis in the genome of Acanthaceae: An in silico approach Kaliswamy, Priyadharsini Vellingiri, Srividhya Nathan, Bharathi Selvaraj, Saravanakumar Pharmacogn Mag Original Article BACKGROUND: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. OBJECTIVE: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. MATERIALS AND METHODS: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. RESULTS: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. CONCLUSION: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future. Medknow Publications & Media Pvt Ltd 2015 /pmc/articles/PMC4329617/ /pubmed/25709226 http://dx.doi.org/10.4103/0973-1296.149731 Text en Copyright: © Pharmacognosy Magazine http://creativecommons.org/licenses/by-nc-sa/3.0 This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Kaliswamy, Priyadharsini
Vellingiri, Srividhya
Nathan, Bharathi
Selvaraj, Saravanakumar
Microsatellite analysis in the genome of Acanthaceae: An in silico approach
title Microsatellite analysis in the genome of Acanthaceae: An in silico approach
title_full Microsatellite analysis in the genome of Acanthaceae: An in silico approach
title_fullStr Microsatellite analysis in the genome of Acanthaceae: An in silico approach
title_full_unstemmed Microsatellite analysis in the genome of Acanthaceae: An in silico approach
title_short Microsatellite analysis in the genome of Acanthaceae: An in silico approach
title_sort microsatellite analysis in the genome of acanthaceae: an in silico approach
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329617/
https://www.ncbi.nlm.nih.gov/pubmed/25709226
http://dx.doi.org/10.4103/0973-1296.149731
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